Physical genomic mapping using restriction endonucleases can provide accurate information about the nucleic acid sequences of various organisms. Optical mapping can be used to produce ordered restriction maps that are visualized using fluorescence microscopy. In optical mapping, nucleic acids are digested by restriction enzymes on a glass surface. The nucleic acids are fixed and elongated on the surface to provide access to restriction sites for the enzymes. Generally, a microchannel is temporarily sealed to a charged glass substrate by mechanical placement, a small volume of nucleic acid solution is flowed into the resulting microchannels, excess nucleic acid solution is removed from the surface/channel interface, followed by the removal of the microchannel to continue processing for optical mapping protocols.
A problem with deposition techniques that use microchannels is that the manual intervention required significantly hinders development of high throughput optical mapping protocols. Further, standard microchannel protocols are not optimal with respect to scalability and automation for high-throughput optical mapping.
Previous attempts to automate the optical mapping process have relied on microfluidic chips that include vents, valves, and pumps. Those chips have many moving parts and have proved to be unreliable and inefficient for fluid movement during the optical mapping process.
There is a need for methods that provide a mechanism of delivering stretched individual nucleic acid molecules to a substrate for high throughput optical mapping.